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Sample GSM5832489 Query DataSets for GSM5832489
Status Public on Sep 04, 2022
Title Sham_CMA_Rep1
Sample type SRA
 
Source name CMA
Organism Rattus norvegicus
Characteristics brain region name: CMA
treatment: Sham
Treatment protocol 2 month old Charles River rats were treated with 18mg/kg body weight of fluoxetine (FT group) or water (Sham group), ad libitum for 6 weeks
Growth protocol Tissue RNA-seq. Brains were removed and frozen immediately on dry ice. Frozen brains were cryosectioned at 250um thickness onto poly-lysine coated slides. The anatomical regions subject to punching were verified using the rat brain atlas of Paxinos and Watson
Extracted molecule polyA RNA
Extraction protocol Frozen, pooled brain tissue punches for each region were thawed on ice in 1 ml Trizol. Tissue was then homogenized using a manual glass douncer with 7-15 slow strokes on ice. RNA was extracted from each replicate sample using the Qiagen RNA Mini kit (Qiagen, Cat# 74104) as per the manufacturer’s instructions with on-column DNase I treatment. RNA quality was examined using a Bioanalyzer 2100 (Agilent technologies, Santa Clara, USA). RNA Integrity Number (RIN) values ranged from 7.1 to 10, with a median value of 9.5. cDNA libraries were prepared using 300 ng of total RNA, from 27 regions in every replicate, using the Illumina TruSeq Stranded Total RNA LT set (Illumina, Cat# RS-122-2301). Paired-end, 76 bp read length RNA-seq was carried out on the Illumina HiSeq 2500 at a depth of 20M reads per sample.
llumina TruSeq Stranded Total RNA LT set (Illumina, Cat# RS-122-2301)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description RNAseq
Data processing RNA-seq data were aligned to the Rattus norvegicus rn5 genome (Rn5 ENSEMBL) with the STAR aligner. Read counts were concurrently calculated using HTseq
Any dataset that failed the default Fastqc sequencing parameters and < 75% mapping rate was discarded.
Genome_build: Rn5
Supplementary_files_format_and_content: fastq and read count files
 
Submission date Jan 24, 2022
Last update date Sep 04, 2022
Contact name Nirmala Arul Rayan
E-mail(s) arulrayan@gis.a-star.edu.sg
Organization name Genome Institute of Singapore
Street address 60 Biopolis Street
City Singapore
ZIP/Postal code 138672
Country Singapore
 
Platform ID GPL18694
Series (1)
GSE194289 Integrative multi-omics landscape of fluoxetine action across 27 brain regions [bulk RNA-seq]
Relations
BioSample SAMN25227401
SRA SRX13884586

Supplementary file Size Download File type/resource
GSM5832489_RRB016-counts.txt.gz 113.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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